Soil rhizospheric metaproteomics is a powerful scientific tool to uncover the interactions between plants and microorganisms in the soil ecosystem. The present study established an extraction method suitable for different soils that could increase the extracted protein content. Close to 1000 separate spots with high reproducibility could be identified in the stained 2-DE gels. Among the spots, 189 spots representing 122 proteins on a 2-DE gel of rice soil samples were successfully identified by MALDI-TOF/TOF-MS. These proteins mainly originated from rice and microorganisms. They were involved in protein, energy, nucleotide, and secondary metabolisms, as well as signal transduction and resistance. Three characteristics of the crop rhizospheric metaproteomics seemed apparent: (1) approximately one-third of the protein spots could not be identified by MALDI-TOF/TOF/MS, (2) the conservative proteins from plants formed a feature distribution of crop rhizospheric metaproteome, and (3) there were very complex interactions between plants and microorganisms existing in a crop rhizospheric soil. Further functional analysis on the identified proteins unveiled various metabolic pathways and signal transductions involved in the soil biotic community. This study provides a paradigm for metaproteomic research on soil biology.

BackgroundPlant WRKY transcription factors play pivotal roles in diverse biological processes but most notably in plant defense response to pathogens. Sheath blight represents one of the predominant diseases in rice. However, our knowledge about the functions of WRKY proteins in rice defense against sheath blight is rather limited.ResultsHere we demonstrate that the expression of Oryza sativa WRKY80 gene (OsWRKY80) is rapidly and strongly induced upon infection of Rhizoctonia solani, the causal agent of rice sheath blight disease. OsWRKY80 expression is also induced by exogenous jasmonic acid (JA) and ethylene (ET), but not by salicylic acid (SA). OsWRKY80-GFP is localized in the nuclei of onion epidermal cells in a transient expression assay. Consistently, OsWRKY80 exhibits transcriptional activation activity in a GAL4 assay in yeast cells. Overexpression of OsWRKY80 in rice plants significantly enhanced disease resistance to R. solani, concomitant with elevated expression of OsWRKY4, another positive regulator in rice defense against R. solani. Suppression of OsWRKY80 by RNA interference (RNAi), on the other hand, compromised disease resistance to R. solani. Results of yeast one-hybrid assay and transient expression assay in tobacco cells have revealed that OsWRKY80 specifically binds to the promoter regions of OsWRKY4, which contain W-box (TTGAC[C/T]) or W-box like (TGAC[C/T]) cis-elements.ConclusionsWe propose that OsWRKY80 functions upstream of OsWRKY4 as an important positive regulatory circuit that is implicated in rice defense response to sheath blight pathogen R. solani.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0137-y) contains supplementary material, which is available to authorized users.

Plant-plant interference is the combined effect of allelopathy, resource competition, and many other factors. Separating allelopathy from resource competition is almost impossible in natural systems but it is important to evaluate the relative contribution of each of the two mechanisms on plant interference. Research on allelopathy in natural and cultivated plant communities has been hindered in the absence of a reliable method that can separate allelopathic effect from resource competition. In this paper, the interactions between allelopathic rice accession PI312777, non-allelopathic rice accession Lemont and barnyardgrass were explored respectively by using a target (rice)-neighbor (barnyardgrass) mixed-culture in hydroponic system. The relative competitive intensity (RCI), the relative neighbor effect (RNE) and the competitive ratio (CR) were used to quantify the intensity of competition between each of the two different potentially allelopathic rice accessions and barnyardgrass. Use of hydroponic culture system enabled us to exclude any uncontrolled factors that might operate in the soil and we were able to separate allelopathy from resource competition between each rice accession and barnyardgrass. The RCI and RNE values showed that the plant-plant interaction was positive (facilitation) for PI312777 but that was negative (competition) for Lemont and barnyardgrass in rice/barnyardgrass mixed-cultures. The CR values showed that one PI312777 plant was more competitive than 2 barnyardgrass plants. The allelopathic effects of PI312777 were much more intense than the resource competition in rice/barnyardgrass mixed cultures. The reverse was true for Lemont. These results demonstrate that the allelopathic effect of PI312777 was predominant in rice/barnyardgrass mixed-cultures. The most significant result of our study is the discovery of an experimental design, target-neighbor mixed-culture in combination with competition indices, can successfully separate allelopathic effects from competition.

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The defense characteristics of allelopathic rice accession PI312777 and its counterpart Lemont induced by exogenous salicylic acid (SA) to suppress troublesome weed barnyardgrass (BYG) were investigated using the methods of suppression subtractive hybridization (SSH) and real-time fluorescence quantitative PCR (qRT-PCR). The results showed that exogenous SA could induce the allelopathic effect of rice on BYG and this inducible defense was SA doserespondent and treatment time-dependent. PI312777 exhibited higher inhibitory effect than Lemont on BYG after treated with different concentrations of SA. The activities of cell protective enzymes including SOD, POD and CAT in the BYG plants co-cultured with PI312777 treated by SA were highly depressed compared with the control (co-cultured with rice without SA-treatment). Similar but lower depression on these enzymes except for CAT was also observed in the BYG plants when co-cultured with Lemont treated by SA. It is therefore suggested that allelopathic rice should be more sensitive than non-allelopathic rice to exogenous SA. Seventeen genes induced by SA were obtained by SSH analysis from PI312777. These genes encode receptor-kinase proteins, ubiquitin carrier proteins, proteins related to phenylpropanoid metabolism, antioxidant related proteins and some growth-mediating proteins. The differential expressions of these genes were validated in part by qRT-PCR in the two rice accessions. Our work elucidated that allelopathic rice possesses an active chemical defense and auto-detoxifying enzyme system such as the up-regulated enzymes involved in de novo biosynthesis of phenolic allelochemicals and the glutathione-S-transferase (GST) associated with xenobiotic detoxification.

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